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Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine - PubMed

  • ️Thu Jan 01 2009

Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine

Oscar Ramírez et al. PLoS One. 2009.

Abstract

Background: Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations. METHODOLOGY/PRINCIPALS FINDINGS: A DNA extraction of a approximately 6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous.

Conclusions: A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Size distribution, plotted in 10 bp bins, of Neandertal , cave bear and Myotragus sequences obtained from metagenomic analyses.

The average hit size in each case is indicated by a dotted line.

Figure 2
Figure 2. The proportion of the Bos genome contained on each chromosome (blue bars) is shown with the proportion of Myotragus sequences (red line) aligning to each Bos chromosome with exactly 1 hit with e-value<1e-3 BLAST.

The observed distribution is not significantly different from the expected one when we compare all the chromosomes together (P = 0.081) or when we tested each one independently and correct for multiple testing.

Figure 3
Figure 3. Maximum-likelihood phylogenetic tree of Myotragus balearicus and other artiodactyls.

The tree was rooted in the cervid Muntiacus reevesi. Numbers along the branches indicate bootstrap support of the maximum-likelihood analyses (first number) and Bayesian support of an independent Bayesian analysis (second number). The scale bar represents 0.01 substitutions/site.

Figure 4
Figure 4. Frequency distribution of 113 Myotragus-specific substitutions observed in 3,602 bp of aligned Ovis, Myotragus and Bos genomic sequences.

Complementary substitutions (such as C to T and G to A) are considered equivalent events. Fisher's exact test was used to calculate the excess of Myotragus-specific C to T and G to A transitions. The total number of each substitution is in parentheses.

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